| --- |
| license: cc-by-4.0 |
| tags: |
| - cryo-em |
| - structural-biology |
| - heterogeneity |
| pretty_name: CryoDynaScape data and results |
| --- |
| |
| # CryoDynaScape: data and results |
|
|
| Data behind the CryoDynaScape manuscript (network-free, hierarchical cryo-EM heterogeneity analysis): every result, |
| model checkpoint and preprocessed input used for the tables and figures. The code will be released on publication. |
|
|
| ## Reproduction |
| Step-by-step instructions for every figure and table: [`docs/REPRODUCE.md`](docs/REPRODUCE.md). Software |
| environments: `envs/`. Exact arguments of every run: `logs/` (and the `args` stored in each checkpoint). The latent |
| behind every AU-FSC evaluation: `results/official/latent_sources.json`. |
|
|
| ## Layout |
| | path | content | |
| |---|---| |
| | `results/` | all runs: bead models, per-particle labels, hierarchy decisions, metrics (`metrics.json`), latents (`*_test_results.h5`), official AU-FSC evaluations (`results/official/<dataset>/score_ext_*.json`, per-query values, generated maps), figure data (`results/figures/`) | |
| | `checkpoints/` | trained CryoDynaScape models per run | |
| | `baselines/inputs/` | baseline inputs prepared from the benchmark datasets (particle stacks, poses, CTF, STAR files) | |
| | `baselines/runs/` | outputs of the published baseline methods (cryoDRGN, RECOVAR, CryoSTAR, cryoSPHERE, DynaMight, e2gmm) | |
| | `data/synth_*` | synthetic benchmark datasets generated for this work | |
| | `data/Spike-MD-128/` | Spike-MD downsampled to 128 px with ground-truth maps of the query frames | |
| | `data/structures/` | atomic models used (PDB 1HZH, 1N0X, 3AVE, 4YBB; AlphaFold3 predictions; IgG templates) | |
| | `logs/`, `envs/`, `notes/`, `docs/` | run logs, environment specs, data notes, reproduction guide | |
| | `data/real/empiar10180_128/`, `data/real/empiar10076_128/` | EMPIAR-10180 and EMPIAR-10076 particles downsampled to 128 px with consensus poses and CTF | |
|
|
| ## Sources and licences of third-party data |
| Derived from CryoBench (Jeon et al. 2024; Zenodo 11629428, 12528292, 14941494; CC BY 4.0), EMPIAR-10180 |
| (Plaschka et al. 2017) and EMPIAR-10076 (Davis et al. 2016), with poses/CTF from the cryoDRGN EMPIAR inputs |
| (Zhong et al.). Full-size original datasets are not re-distributed here; obtain them from those sources. |
| Our own data are released under CC BY 4.0. |
|
|
